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- PDB-3oxh: Mycobacterium tuberculosis kinase inhibitor homolog RV0577 -

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Basic information

Entry
Database: PDB / ID: 3oxh
TitleMycobacterium tuberculosis kinase inhibitor homolog RV0577
ComponentsRV0577 PROTEIN
KeywordsHYDROLASE INHIBITOR / KINASE REGULATION / ANTIBIOTIC RESISTANCE / MYCOBACTERIUM TUBERCULOSIS / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TBSGC / BABBB fold
Function / homology
Function and homology information


: / extracellular region / plasma membrane
Similarity search - Function
Glyoxalase-like domain, group 6 / Glyoxalase-like domain / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
PARA-MERCURY-BENZENESULFONIC ACID / Xylitol / Putative glyoxylase CFP32 / Putative glyoxylase CFP32
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsEchols, N. / Flynn, E.M. / Stephenson, S. / Ng, H.-L. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Biochemistry / Year: 2017
Title: Structural and Biophysical Characterization of the Mycobacterium tuberculosis Protein Rv0577, a Protein Associated with Neutral Red Staining of Virulent Tuberculosis Strains and Homologue of ...Title: Structural and Biophysical Characterization of the Mycobacterium tuberculosis Protein Rv0577, a Protein Associated with Neutral Red Staining of Virulent Tuberculosis Strains and Homologue of the Streptomyces coelicolor Protein KbpA.
Authors: Buchko, G.W. / Echols, N. / Flynn, E.M. / Ng, H.L. / Stephenson, S. / Kim, H.B. / Myler, P.J. / Terwilliger, T.C. / Alber, T. / Kim, C.Y.
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Other
Revision 1.2Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RV0577 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2185
Polymers29,6371
Non-polymers5814
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.597, 81.981, 36.037
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RV0577 PROTEIN


Mass: 29637.268 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: cfp30B, MT0606, MTV039.15, Rv0577, TB27.3 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A5N8, UniProt: P9WIR3*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PMB / PARA-MERCURY-BENZENESULFONIC ACID


Mass: 357.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5HgO3S
#4: Sugar ChemComp-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H12O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe residue at position 257 is confirmed to be an ALA. This could be reflective of the genomic DNA ...The residue at position 257 is confirmed to be an ALA. This could be reflective of the genomic DNA the protein was cloned from or a polymerase error.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 1.1M NACITRATE, 4% BUTANOL, MES, PH 6.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.3.111.0094
SYNCHROTRONALS 8.3.120.97949, 0.97965, 1.00801
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 9, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YSINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.00941
20.979491
30.979651
41.008011
ReflectionResolution: 1.75→20 Å / Num. obs: 25186 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 18.88 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 23.125
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.04 / Rsym value: 0.56 / % possible all: 98.9

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0005refinement
ADSCdata collection
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.246 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1230 4.9 %RANDOM
Rwork0.176 ---
obs0.178 25186 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.874 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--0.55 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 23 271 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221926
X-RAY DIFFRACTIONr_bond_other_d0.0010.021692
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9492631
X-RAY DIFFRACTIONr_angle_other_deg0.7783.0013920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39624.93375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06415263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.667154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
X-RAY DIFFRACTIONr_nbd_refined0.2070.2402
X-RAY DIFFRACTIONr_nbd_other0.1840.21699
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2937
X-RAY DIFFRACTIONr_nbtor_other0.0860.21086
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.5320.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9881.51318
X-RAY DIFFRACTIONr_mcbond_other0.1961.5514
X-RAY DIFFRACTIONr_mcangle_it1.30621989
X-RAY DIFFRACTIONr_scbond_it2.1063767
X-RAY DIFFRACTIONr_scangle_it2.964.5642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.84 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.235 180 -
Rwork0.213 3335 -
obs--98.21 %
Refinement TLS params.Method: refined / Origin x: 23.2861 Å / Origin y: 19.4825 Å / Origin z: 10.3077 Å
111213212223313233
T-0.0887 Å20.0105 Å2-0.0033 Å2--0.0956 Å20.0139 Å2---0.1224 Å2
L2.1191 °20.7197 °2-0.6666 °2-1.3752 °2-0.0954 °2--0.9636 °2
S-0.124 Å °0.0624 Å °-0.0589 Å °-0.069 Å °0.0559 Å °-0.0497 Å °0.019 Å °0.0222 Å °0.0681 Å °

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